|importing transition only data to scan for PTM diagnostic ions||janelle hancock||2022-08-16|
Dear Skyline developers,
We would like to be able to identify scans in which particular diagnostic ions occur, regardless of the precursor. Our modifications are Lysine linked ubiquitin or Sumo type peptide remnants. The mods are 4-6 amino acids long. We are running an Q exactive HF in standard TopN DDA mode. The modification itself is a peptide, and upon HCD fragmentation produces a predictable pattern on neutral losses (which remain attached to the parent peptide) and released diagnostic b ions. I've attached an example spreadsheet of one such tryptic remnant, from tryptic digest of the human sumo-like protein UFM1.
The spectra for these modified peptides is normally quite complex and we don't get many good matches using PD or maxquant. If possible I would like to use skyline to identify what scans contain these diagnostic b-ions. Once I know that, I can make an inclusion list to re-run the same samples, acquire better quality spectra, enabling us to get and ID and modification site assignment.
Can you please tell me if I can use skyline to analyze transitions only, without considering what precursor they came from?